BUG: Use GenerateOutputInformation and pipeline isolation

The TransformGeometryImageFilter::GenerateData method was refactored
for correct pipeline behavior. The output Image's meta-data is
correctly modifed in the GenerateOutputInformation method, so that
down stream filters can uses the information. The composite pipeline
is not isolated from the inputs and output using the double graft
convention. However, only the bulk data pointer and buffered region
are copied to the output, as not to change the geometry information
previously set.

Modules/Core/Transform/include/itkTransformGeometryImageFilter.h

@@ -142,18 +142,20 @@ class ITK_TEMPLATE_EXPORT TransformGeometryImageFilter : public ImageToImageFilt
   using RigidTransformType = VersorRigid3DTransform<double>;
   using RigidTransformConstPointer = typename RigidTransformType::ConstPointer;
 
-  /** Set/Get rigid transform. The default is an identity transform */
+  /** Set/Get required rigid transform. */
   itkSetGetDecoratedObjectInputMacro(RigidTransform, RigidTransformType);
 
   /** Set/Get required input image. (A wrapper to this->Set/GetInput()) */
   itkSetInputMacro(InputImage, InputImageType);
-
   itkGetInputMacro(InputImage, InputImageType);
 
 protected:
   TransformGeometryImageFilter();
   ~TransformGeometryImageFilter() override = default;
 
+  void
+  GenerateOutputInformation() override;
+
   void
   GenerateData() override;
 };

Modules/Core/Transform/include/itkTransformGeometryImageFilter.hxx

@@ -33,51 +33,60 @@ TransformGeometryImageFilter<TInputImage, TOutputImage>::TransformGeometryImageF
 
   // "RigidTransform" required ( not numbered )
   Self::AddRequiredInputName("RigidTransform");
-
-  // initialize transform
 }
 
 
 template <typename TInputImage, typename TOutputImage>
 void
-TransformGeometryImageFilter<TInputImage, TOutputImage>::GenerateData()
+TransformGeometryImageFilter<TInputImage, TOutputImage>::GenerateOutputInformation()
 {
-  if (!this->GetInput())
-  {
-    itkExceptionMacro(<< "Input image has not been connected");
-    return;
-  }
 
-  typename OutputImageType::Pointer outputPtr;
+  Superclass::GenerateOutputInformation();
 
-  //  SEE HEADER FILE FOR MATH DESCRIPTION
-
-  {
-    /** make a cast copied version of the input image **/
-    using DuplicatorType = CastImageFilter<InputImageType, OutputImageType>;
-    typename DuplicatorType::Pointer CastFilter = DuplicatorType::New();
-    CastFilter->SetInput(this->GetInput());
-    CastFilter->Update();
-    outputPtr = CastFilter->GetOutput();
-  }
+  OutputImageType *      outputPtr = this->GetOutput();
+  const InputImageType * inputPtr = this->GetInputImage();
 
+  //  SEE HEADER FILE FOR MATH DESCRIPTION
   RigidTransformConstPointer                    FMTxfm = this->GetRigidTransform();
   const typename RigidTransformType::MatrixType inverseRotation(FMTxfm->GetMatrix().GetInverse());
 
   // Modify the origin and direction info of the image to reflect the transform.
-  itk::Vector<double, 3> newOriginVector =
-    inverseRotation * (this->GetInput()->GetOrigin().GetVectorFromOrigin() - FMTxfm->GetCenter().GetVectorFromOrigin() -
+  Vector<double, 3> newOriginVector =
+    inverseRotation * (inputPtr->GetOrigin().GetVectorFromOrigin() - FMTxfm->GetCenter().GetVectorFromOrigin() -
                        FMTxfm->GetTranslation()) // NewOrigin = [R^-1] * ( O - C - T ) + C
     + FMTxfm->GetCenter().GetVectorFromOrigin();
-  itk::Point<double, 3> newOriginPoint;
+  Point<double, 3> newOriginPoint;
   for (int i = 0; i < 3; ++i)
   {
     newOriginPoint[i] = newOriginVector[i];
   }
   outputPtr->SetOrigin(newOriginPoint);
-  outputPtr->SetDirection(inverseRotation * this->GetInput()->GetDirection()); // NewDC = [R^-1][DC]
+  outputPtr->SetDirection(inverseRotation * inputPtr->GetDirection()); // NewDC = [R^-1][DC]
+}
+
+
+template <typename TInputImage, typename TOutputImage>
+void
+TransformGeometryImageFilter<TInputImage, TOutputImage>::GenerateData()
+{
+  OutputImageType * output = this->GetOutput();
+
+  auto input = InputImageType::New();
+  input->Graft(const_cast<InputImageType *>(this->GetInput()));
+
+  //  SEE HEADER FILE FOR MATH DESCRIPTION
+
+  /** make a cast copied version of the input image **/
+  using DuplicatorType = CastImageFilter<InputImageType, OutputImageType>;
+  typename DuplicatorType::Pointer castFilter = DuplicatorType::New();
+  castFilter->SetInput(input);
+
+  castFilter->GraftOutput(this->GetOutput());
+  castFilter->Update();
+
 
-  this->GraftOutput(outputPtr);
+  // Can't use graft as it will overwrite the new meta-data
+  output->SetPixelContainer(castFilter->GetOutput()->GetPixelContainer());
 }
 
 } // end namespace itk